Some people have an adverse reaction to the protein in wheat flour when it is eaten. The problem mainly affects people who have coeliac disease, which is associated with wheat gluten. It is estimated that about 1% of the UK population suffers from coeliac disease. Other adverse reactions to wheat are quite rare. The evidence suggests that consumers over-estimate food allergies and intolerances by a factor of 10, meaning the prevalence is ten times less than it is perceived.

Legislation requires the clear labelling of food allergens so that sufferers can avoid foods to which they are allergic. Wheat, wheat flour and gluten should all be clearly labelled when they are present in foods.

Flour is also sometimes associated with asthma (bakers asthma). A maximum exposure limit for flour dust is established in UK workplaces and flour mills have worked hard over the years to ensure that flour is kept enclosed in the milling process so that exposure to dust is minimised.